The Galactic Arcade [v1]

Miis can now be used in Super Smash Brothers.

Time had an interview with miyamoto who confirmed that yes, star fox is coming to wii u and they've been working on it for half a year, there were also pictures and if you see the screen behind him in the e3 direct you'll see it

Besides having Mii's in the game, the new toys (amiibo) were featured for Smash Brothers. They have stats and stuff which can be leveled up and upgraded, meaning that they will have their own individual data depending on how you play them. Toys will also be incorporated into more games in the future.
Bayonetta 2 will include the first Bayonetta, and it looked like there was some special Nintendo character themed costumes (like Link and Samus).
Next Zelda game will be open world.
More info on next Yoshi game: Yoshi's Woolly World. Uses yarn everywhere.
New Kirby game for Wii U: Kirby and the Rainbow Curse.
Brief look at Pokémon OR/AS featuring the starters and the new megas. Also a look at new forms (megas?) of Groudon and Kyogre.
New Xenoblade Chronicles game coming soon.
New Mario level maker game where you can create levels from classic Super Mario Brothers to New Super Mario Brothers.
In the Mario category, a new game called Captain Toad: Treasure Tracker will feature Captain Toad as the main character playing through levels from Super Mario 3d World.
Hyrule Warriors detailed, with Zelda, Impa, and Midna as playable characters in addition to Link.
Splatoon, a new shooter-like game coming to Wii U has you as a character who can change from a human to a squid. Goal is to cover area with as much ink as possible. Gameplay in 4 vs. 4 online multiplayer.
Finally, Palutena from Kid Icarus confirmed for Super Smash Brothers.

I think that's about it, other than the crazy claymation stuff throughout and opening fighting scene between Reggie and Iwata.